M. Gilson

发表

Multiple‐site titration and molecular modeling: Two rapid methods for computing energies and forces for ionizable groups in proteins

M. Gilson, 1993, Proteins.

Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program

L. R. Scott, J. Madura, M. Gilson, 1995 .

Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis

B. Honig, M. Gilson, 1988, Proteins.

Calculating the electrostatic potential of molecules in solution: Method and error assessment

K. Sharp, B. Honig, M. Gilson, 1988 .

On the calculation of electrostatic interactions in proteins.

B. Honig, M. Gilson, A. Rashin, 1985, Journal of molecular biology.

Calculation of electrostatic potentials in an enzyme active site

B. Honig, M. Gilson, 1987, Nature.

BMC Biology BioMed Central

Gary D Bader, Antony F. Quinn, Peter M Woollard, 2007 .

Public domain databases for medicinal chemistry.

M. Gilson, G. Nicola, Tiqing Liu, 2012, Journal of medicinal chemistry.

The determinants of pKas in proteins.

M. Gilson, J. Antosiewicz, J. Mccammon, 1996, Biochemistry.

Computing ionization states of proteins with a detailed charge model

M. Gilson, A. Elcock, J. Briggs, 1996, J. Comput. Chem..

A new class of models for computing receptor-ligand binding affinities.

M. Gilson, M. Head, J. Given, 1997, Chemistry & biology.

Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm.

M. Gilson, Chia-En Chang, 2004, Journal of the American Chemical Society.

Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design.

M. Gilson, Chia-En Chang, Wei Chen, 2004, Biophysical journal.

The statistical-thermodynamic basis for computation of binding affinities: a critical review.

M. Gilson, J. Mccammon, J. Given, 1997, Biophysical journal.

Configurational entropy in protein-peptide binding: computational study of Tsg101 ubiquitin E2 variant domain with an HIV-derived PTAP nonapeptide.

Yuan-Ping Pang, Michael K Gilson, Sandeep Somani, 2009, Journal of molecular biology.

Correlation as a Determinant of Configurational Entropy in Supramolecular and Protein Systems

Andrew T. Fenley, M. Gilson, V. Hnizdo, 2014, The journal of physical chemistry. B.

Biological Applications of Electrostatic Calculations and Brownian Dynamics Simulations

J. Andrew McCammon, Michael K. Gilson, Brock A. Luty, 2007 .

Electrostatic interactions in proteins.

K. Sharp, B. Honig, M. Gilson, 1987, Progress in clinical and biological research.

Thermodynamic linkage between the binding of protons and inhibitors to HIV‐1 protease

Joanna Trylska, Jan Antosiewicz, Maciej Geller, 2008, Protein science : a publication of the Protein Society.

Ligand configurational entropy and protein binding

M. Gilson, Chia-En Chang, Wei Chen, 2007, Proceedings of the National Academy of Sciences.

The physical basis of nucleic acid base stacking in water.

M. Gilson, R. Luo, H. Gilson, 2001, Biophysical journal.

Nucleic acid base-pairing and N-methylacetamide self-association in chloroform: affinity and conformation.

M. Gilson, M. Head, J. Given, 1999, Biophysical chemistry.

Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model.

M. Gilson, H. Muddana, 2012, Journal of chemical theory and computation.

Attach-Pull-Release Calculations of Ligand Binding and Conformational Changes on the First BRD4 Bromodomain

Niel M. Henriksen, M. Gilson, G. Heinzelmann, 2017, Journal of chemical theory and computation.

Calculation of protein-ligand binding affinities.

M. Gilson, Huan‐Xiang Zhou, 2007, Annual review of biophysics and biomolecular structure.

Small Molecule pKa Prediction with Continuum Electrostatics Calculations

M. Gilson, J. Mccammon, M. Potter, 1994 .

Prediction of pH-dependent properties of proteins.

M. Gilson, J. Antosiewicz, J. Mccammon, 1994, Journal of molecular biology.

Calculation of Molecular Configuration Integrals

M. Gilson, Chia-En Chang, M. Potter, 2003 .

Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril–Guest Binding Enthalpies

Andrew T. Fenley, Niel M. Henriksen, M. Gilson, 2014, Journal of chemical theory and computation.

Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics.

Andrew T. Fenley, Niel M. Henriksen, M. Gilson, 2015, The journal of physical chemistry. B.

Computational Calorimetry: High-Precision Calculation of Host–Guest Binding Thermodynamics

Andrew T. Fenley, Niel M. Henriksen, M. Gilson, 2015, Journal of chemical theory and computation.

Parameterization of an effective potential for protein–ligand binding from host–guest affinity data

M. Gilson, R. Levy, E. Gallicchio, 2016, Journal of molecular recognition : JMR.

Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host–Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters

Niel M. Henriksen, M. Gilson, 2017, Journal of chemical theory and computation.

Motor-like Properties of Nonmotor Enzymes.

M. Gilson, D. Slochower, 2018, Biophysical journal.

Motor-Like Properties of Non-Motor Enzymes

M. Gilson, D. Slochower, 2017, bioRxiv.

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

Niel M. Henriksen, D. Mobley, M. Shirts, 2019, bioRxiv.

''Mining minima'': Direct computation of conformational free energy

Michael K. Gilson, Martha S. Head, James A. Given, 1997 .

Extraction of configurational entropy from molecular simulations via an expansion approximation.

Michael K Gilson, M. Gilson, B. Killian, 2007, The Journal of chemical physics.

Theory of free energy and entropy in noncovalent binding.

Michael K. Gilson, Huan-Xiang Zhou, M. Gilson, 2009, Chemical reviews.

Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril.

Michael K Gilson, M. Gilson, C. Nguyen, 2012, The Journal of chemical physics.

Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa

Michael K. Gilson, Tom Kurtzman, M. Gilson, 2014, Journal of chemical theory and computation.

Simulating Water Exchange to Buried Binding Sites.

M. Gilson, R. Walker, Tom Kurtzman, 2018, Journal of chemical theory and computation.

Entropy–enthalpy transduction caused by conformational shifts can obscure the forces driving protein–ligand binding

Andrew T. Fenley, Michael K Gilson, Andrew T Fenley, 2012, Proceedings of the National Academy of Sciences.

Spatial Decomposition of Translational Water–Water Correlation Entropy in Binding Pockets

M. Gilson, Tom Kurtzman, C. Nguyen, 2015, Journal of chemical theory and computation.

The binding database: overview and user's guide.

X Chen, M K Gilson, M. Gilson, 2001, Biopolymers.

Dynamic architecture of a protein kinase

Christopher L. McClendon, Susan S. Taylor, M. Gilson, 2014, Proceedings of the National Academy of Sciences.

Energetics of charge–charge interactions in proteins

M K Gilson, B. Honig, M. Gilson, 1988, Proteins.

The dielectric constant of a folded protein

M K Gilson, B. Honig, M. Gilson, 1986, Biopolymers.

pKa Shifts in Small Molecules and HIV Protease: Electrostatics and Conformation

Michael K. Gilson, Martha S. Head, John Moult, 1998 .

Theoretical and experimental analysis of ionization equilibria in ovomucoid third domain.

M K Gilson, M. Gilson, J. Antosiewicz, 1998, Biochemistry.

A synthetic host-guest system achieves avidin-biotin affinity by overcoming enthalpy–entropy compensation

Michael K. Gilson, Tadashi Mori, Angel E. Kaifer, 2007, Proceedings of the National Academy of Sciences.

New ultrahigh affinity host-guest complexes of cucurbit[7]uril with bicyclo[2.2.2]octane and adamantane guests: thermodynamic analysis and evaluation of M2 affinity calculations.

Michael K Gilson, Yoshihisa Inoue, Young Ho Ko, 2011, Journal of the American Chemical Society.

The electrostatic response of water to neutral polar solutes: implications for continuum solvent modeling.

Andrew T. Fenley, Michael K Gilson, Neil V Sapra, 2013, The Journal of chemical physics.

Comparison of generalized born and poisson models: Energetics and dynamics of HIV protease

Ray Luo, Laurent David, M. Gilson, 2000 .

A hierarchical method for generating low‐energy conformers of a protein‐ligand complex

M. Gilson, J. Given, Michael K. Gilson, 1998, Proteins.

MODELING THE PHYSICAL CHEMISTRY OF BINDING : FORCES AND FLEXIBILITY

M. Gilson, Huan‐Xiang Zhou, 2007 .

Optimized Mapping of Gas-Phase Quantum Calculations to General Force Field Lennard-Jones Parameters Based on Liquid-State Data

Niel M. Henriksen, M. Gilson, Lee‐Ping Wang, 2019 .

Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation

M. Gilson, G. Heinzelmann, 2021, Scientific Reports.

Data-driven analysis of the number of Lennard–Jones types needed in a force field

M. Gilson, Lee‐Ping Wang, M. Schauperl, 2020, Communications Chemistry.

Coordinate Systems and the Calculation of Molecular Properties

M. Gilson, M. Potter, 2002 .

openforcefield/openforcefields: Version 1.2.0 "Parsley" Update

Daniel G. A. Smith, Caitlin C. Bannan, D. Mobley, 2020 .

Structural model for an AxxxG-mediated dimer of surfactant-associated protein C.

M. Gilson, V. Kairys, B. Luy, 2004, European journal of biochemistry.

A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site

D. Case, M. Gilson, A. Kovalenko, 2019, PloS one.

Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative

Niel M. Henriksen, D. Mobley, M. Gilson, 2019 .

Evaluation of Representations and Response Models for Polarizable Force Fields

Andrew T. Fenley, M. Gilson, Alexey Voronin, 2016, The journal of physical chemistry. B.

The Determinants of p K as in Proteins †

M. Gilson, J. Antosiewicz, J. Mccammon, 2022 .

LIMO: Latent Inceptionism for Targeted Molecule Generation

M. Gilson, Rose Yu, P. Eckmann, 2022, ICML.

Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations.

M. Gilson, W. Sherman, Zhixiong Lin, 2020, Journal of chemical theory and computation.

Mechanistic analysis of light-driven overcrowded alkene-based molecular motors by multiscale molecular simulations.

M. Gilson, Mudong Feng, 2020, Physical chemistry chemical physics : PCCP.

The Fundamental Role of Flexibility on the Strength of Molecular Binding.

M. Gilson, J. Douglas, Christopher Forrey, 2012, Soft matter.

Toward Expanded Diversity of Host–Guest Interactions via Synthesis and Characterization of Cyclodextrin Derivatives

M. Gilson, B. Duggan, K. Kellett, 2018, Journal of Solution Chemistry.

Data-driven analysis of the number of Lennard–Jones types needed in a force field

M. Gilson, Lee‐Ping Wang, M. Schauperl, 2020, Communications Chemistry.

D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

Rommie E. Amaro, M. Gilson, W. P. Walters, 2019, Journal of Computer-Aided Molecular Design.

Accelerated convergence of molecular free energy via superposition approximation-based reference states.

M. Gilson, Sandeep Somani, 2011, The Journal of chemical physics.

Toward Learned Chemical Perception of Force Field Typing Rules.

Caitlin C. Bannan, D. Mobley, M. Shirts, 2018, Journal of chemical theory and computation.

Configurational Entropy in Protein-Peptide Binding. Computational Study of Tsg101 UEV Domain with an HIV-derived PTAP Nonapeptide

M. Gilson, Y. Pang, B. Killian, 2009 .

Hydrosomes: Optically trapped femtoliter containers for single molecule studies and microfluidics

M. Gilson, A. M. Crawford, L. Goldner, 2005, physics/0510196.

Comparison of generalized born and poisson models: Energetics and dynamics of HIV protease

M. Gilson, R. Luo, L. David, 2000, J. Comput. Chem..

Force Field Partial Charges with Restrained Electrostatic Potential 2 (RESP2)

D. Mobley, M. Gilson, C. Bayly, 2019 .

Structural insights into the gating of DNA passage by the topoisomerase DNA-gate.

M. Gilson, Jung-Hsin Lin, N. Chan, 2018 .

Binding of tacrine and 6-chlorotacrine by acetylcholinesterase.

T. Straatsma, M. Gilson, J. Briggs, 1996, Biopolymers.

Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo

Teresa Danielle Bergazin, D. Mobley, M. Gilson, 2020, Journal of Computer-Aided Molecular Design.

Enhancing Water Sampling of Buried Binding 1 Sites Using Nonequilibrium Candidate Monte 2 Carlo 3

Teresa Danielle Bergazin, D. Mobley, M. Gilson, 2020 .

Protein-ligand binding enthalpies from near-millisecond simulations: Analysis of a preorganization paradox.

M. Gilson, Amanda Li, A. Li, 2018, The Journal of chemical physics.

Development and Benchmarking of 1 Open Force Field v1.0.0, the Parsley 2 small molecule force ﬁeld 3

Daniel G. A. Smith, Chaya D. Stern, Caitlin C. Bannan, 2020 .

HYDROPHOBE Challenge: A Joint Experimental and Computational Study on the Host-Guest Binding of Hydrocarbons to Cucurbiturils, Allowing Explicit Evaluation of Guest Hydration Free-Energy Contributions.

Niel M. Henriksen, M. Gilson, Andreas Hansen, 2017, The journal of physical chemistry. B.

Virtual Screening of Molecular Databases Using a Support Vector Machine.

M. Gilson, R. Jorissen, 2005 .

Evaluating the Substrate-Envelope Hypothesis: Structural Analysis of Novel HIV-1 Protease Inhibitors Designed To Be Robust against Drug Resistance

Michael K. Gilson, Hong Cao, Bruce Tidor, 2010, Journal of Virology.

Evaluation and Minimization of Uncertainty in ITC Binding Measurements: Heat Error, Concentration Error, Saturation, and Stoichiometry.

Niel M. Henriksen, M. Gilson, S. Kantonen, 2017, Biochimica et biophysica acta. General subjects.

Accelerated Poisson–Boltzmann calculations for static and dynamic systems

Ray Luo, Michael K. Gilson, Laurent David, 2002, J. Comput. Chem..

Attractive Interactions between Heteroallenes and the Cucurbituril Portal.

M. Gilson, E. Keinan, O. Reany, 2017, Journal of the American Chemical Society.

Comparing Ligand Interactions with Multiple Receptors via Serial Docking

Michael K. Gilson, Miguel X. Fernandes, Visvaldas Kairys, 2004, J. Chem. Inf. Model..

Host-guest complexes with protein-ligand-like affinities: computational analysis and design.

Michael K Gilson, Yoshihisa Inoue, M. Gilson, 2009, Journal of the American Chemical Society.

Accounting for apparent deviations between calorimetric and van't Hoff enthalpies.

Niel M. Henriksen, M. Gilson, S. Kantonen, 2017, Biochimica et biophysica acta. General subjects.

Probing the orientation of inhibitor and epoxy-eicosatrienoic acid binding in the active site of soluble epoxide hydrolase.

Niel M. Henriksen, M. Gilson, Jun Yang, 2017, Archives of biochemistry and biophysics.

ConCept: de Novo Design of Synthetic Receptors for Targeted Ligands

Michael K. Gilson, Wei Chen, M. Gilson, 2007, J. Chem. Inf. Model..

Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST

Michael K. Gilson, Ross C. Walker, Tom Kurtzman, 2016, J. Comput. Chem..

On the theory of noncovalent binding.

Michael K Gilson, M. Gilson, M. Mihăilescu, 2004, Biophysical journal.

Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field.

Daniel G. A. Smith, Chaya D. Stern, Caitlin C. Bannan, 2020, Journal of chemical theory and computation.

D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

Shuai Liu, Huanwang Yang, Stephen K. Burley, 2017, Journal of Computer-Aided Molecular Design.

Competition between intra- and intermolecular hydrogen bonding : Effect on para/ortho adsorptive selectivity for substituted phenols

M. Gilson, G. Payne, K. Mardis, 2000 .

Solution structure and functional ligand screening of HI0719, a highly conserved protein from bacteria to humans in the YjgF/YER057c/UK114 family.

M. Gilson, J. Orban, E. Eisenstein, 2003, Biochemistry.

Improving the Efficiency and Activity of Electrocatalysts for the Reduction of CO2 through Supramolecular Assembly with Amino Acid-Modified Ligands.

M. Gilson, C. Kubiak, Jian Yin, 2016, Journal of the American Chemical Society.

Peptides Displayed as High Density Brush Polymers Resist Proteolysis and Retain Bioactivity

M. Gilson, A. M. Rush, N. Gianneschi, 2014, Journal of the American Chemical Society.

Proflavine acts as a Rev inhibitor by targeting the high-affinity Rev binding site of the Rev responsive element of HIV-1.

M. Gilson, Chia-En Chang, J. Marino, 2003, Biochemistry.

Improving Structure-Based Virtual Screening with Ensemble Docking and Machine Learning

Carlos A. Brizuela, Michael K. Gilson, Joel Ricci-Lopez, 2021, J. Chem. Inf. Model..

Predicting binding free energies: Frontiers and benchmarks

David L. Mobley, Michael K. Gilson, D. Mobley, 2016, bioRxiv.

BindingDB: a web-accessible database of experimentally determined protein–ligand binding affinities

Xin Wen, Michael K. Gilson, Tiqing Liu, 2006, Nucleic Acids Res..

Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking

Jeffrey R. Wagner, Christopher Churas, Shuai Liu, 2018, bioRxiv.

Enhanced Diffusion and Chemotaxis of Enzymes.

M. Gilson, Mudong Feng, 2019, Annual review of biophysics.

A Thermodynamic Limit on the Role of Self-Propulsion in Enhanced Enzyme Diffusion.

M. Gilson, Mudong Feng, 2019, Biophysical journal.

A Thermodynamic Limit on the Role of Self-Propulsion in Enhanced Enzyme Diffusion

M. Gilson, Mudong Feng, 2018 .

A Thermodynamic Limit on the Role of Self-Propulsion in Enhanced Enzyme Diffusion

M. Gilson, Mudong Feng, 2018, bioRxiv.

Open "back door" in a molecular dynamics simulation of acetylcholinesterase.

J L Sussman, J A McCammon, I Silman, 1994, Science.

Escaping Atom Types in Force Fields Using Direct Chemical Perception.

David L Mobley, Michael R Shirts, Michael K Gilson, 2018, Journal of chemical theory and computation.

Open Force Field Consortium: Escaping atom types using direct chemical perception with SMIRNOFF v0.1

David L. Mobley, Michael K. Gilson, Christopher I. Bayly, 2018, bioRxiv.

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Jian Yin, David L. Mobley, Michael K. Gilson, 2016, Journal of Computer-Aided Molecular Design.

Theory of electrostatic interactions in macromolecules.

M K Gilson, M. Gilson, 1995, Current opinion in structural biology.

Antitumor Activity of 1,18-Octadecanedioic Acid-Paclitaxel Complexed with Human Serum Albumin

Niel M. Henriksen, Christopher V. Barback, M. Gilson, 2019, Journal of the American Chemical Society.

Testing inhomogeneous solvation theory in structure-based ligand discovery

Michael K Gilson, Tom Kurtzman, Brian K Shoichet, 2017, Proceedings of the National Academy of Sciences.

Protein folding and binding: from biology to physics and back again.

Michael K Gilson, Sheena E Radford, S. Radford, 2011, Current opinion in structural biology.

Minimum information about a bioactive entity (MIABE)

Peter Murray-Rust, John P. Overington, Henning Hermjakob, 2011, Nature Reviews Drug Discovery.

Ten Years of Standardizing Proteomic Data: A Report on the HUPO‐PSI Spring Workshop

Henning Hermjakob, Andrew R Jones, Pierre-Alain Binz, 2012, Proteomics.

BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology

Michael K. Gilson, Michael Baitaluk, Tiqing Liu, 2015, Nucleic Acids Res..

Fast Equilibration of Water between Buried Sites and Bulk by MD with Parallel Monte Carlo Water Moves on GPUs

M. Gilson, W. Sherman, I. Ben-Shalom, 2021 .

The minimum information required for reporting a molecular interaction experiment (MIMIx)

Peter Woollard, Mark Gerstein, Gary D Bader, 2007, Nature Biotechnology.

Acetylcholinesterase: diffusional encounter rate constants for dumbbell models of ligand.

M. Gilson, J. Antosiewicz, J. Mccammon, 1995, Biophysical journal.

Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate

M. Gilson, Jung-Hsin Lin, N. Chan, 2018, Nature Communications.

Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation

J. Andrew McCammon, Michael K. Gilson, Brock A. Luty, 1993 .

Structure-Based Experimental Datasets for Benchmarking of Protein Simulation Force Fields

Vincent A. Voelz, D. Mobley, M. Wall, 2023, 2303.11056.

Ligand-receptor docking with the Mining Minima optimizer

Ray Luo, Michael K. Gilson, Laurent David, 2001, J. Comput. Aided Mol. Des..

Modeling protonation equilibria in biomolecules

M. Gilson, 1997 .

Computer Modeling of Acetylcholinesterase and Acetylcholinesterase-Ligand Complexes

L. R. Scott, M. Gilson, J. Antosiewicz, 1995 .

Binding of Cations and Protons in the Active Site of Acetylcholinesterase

M. Gilson, J. Antosiewicz, S. Wlodek, 1995 .

Acetylcholinesterase: Effects of Ionic Strength and Dimerization on the Rate Constants

M. Gilson, J. Antosiewicz, J. Mccammon, 1994 .

Overview of the SAMPL6 host–guest binding affinity prediction challenge

David L. Mobley, Michael Chiu, Michael K. Gilson, 2018, bioRxiv.

Overview of the SAMPL6 host-guest binding affinity prediction challenge

Wei Yao, David L. Mobley, Michael K. Gilson, 2018, bioRxiv.

Blind prediction of cyclohexane–water distribution coefficients from the SAMPL5 challenge

David L. Mobley, Michael Chiu, Michael K. Gilson, 2016, Journal of Computer-Aided Molecular Design.

Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2)

D. Mobley, M. Gilson, C. Bayly, 2020, Communications Chemistry.

Destabilization of an alpha-helix-bundle protein by helix dipoles.

B. Honig, M. Gilson, 1989, Proceedings of the National Academy of Sciences of the United States of America.

Substrate-driven chemotactic assembly in an enzyme cascade.

M. Gilson, S. Benkovic, Ayusman Sen, 2018, Nature chemistry.

Robust against Drug Resistance HIV-1 Protease Inhibitors Designed To Be Hypothesis: Structural Analysis of Novel Evaluating the Substrate-Envelope

B. Tidor, M. Gilson, C. Schiffer, 2014 .

Interpreting trends in the binding of cyclic ureas to HIV-1 protease.

M K Gilson, M. Gilson, R. Luo, 2001, Journal of molecular biology.

The Carmaphycins: New Proteasome Inhibitors Exhibiting an α,β‐Epoxyketone Warhead from a Marine Cyanobacterium

Andrew T. Fenley, M. Gilson, B. Moore, 2012, Chembiochem : a European journal of chemical biology.

Virtual Screening of Molecular Databases Using a Support Vector Machine

Michael K. Gilson, Robert N. Jorissen, M. Gilson, 2005, J. Chem. Inf. Model..

Ions and inhibitors in the binding site of HIV protease: comparison of Monte Carlo simulations and the linearized Poisson-Boltzmann theory.

M. Gilson, B. Eisenberg, D. Henderson, 2009, Biophysical journal.

SuperTarget goes quantitative: update on drug–target interactions

Philip E. Bourne, Michael K. Gilson, Jessica Ahmed, 2011, Nucleic Acids Res..

Overview of the SAMPL5 host–guest challenge: Are we doing better?

Jian Yin, David L. Mobley, Michael Chiu, 2016, Journal of Computer-Aided Molecular Design.

D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings

Huanwang Yang, Stephen K. Burley, W. Patrick Walters, 2018, Journal of Computer-Aided Molecular Design.

D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions

Shuai Liu, Huanwang Yang, Stephen K. Burley, 2016, Journal of Computer-Aided Molecular Design.

BindingDB: a web-accessible molecular recognition database.

X Chen, M Liu, M K Gilson, 2001, Combinatorial chemistry & high throughput screening.

Entropic effects enable life at extreme temperatures

M. Gilson, D. Sept, Kaifu Gao, 2019, Science Advances.

The inclusion of electrostatic hydration energies in molecular mechanics calculations

Michael K. Gilson, Barry Honig, B. Honig, 1991, J. Comput. Aided Mol. Des..

Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces.

Lauren Wickstrom, Michael K Gilson, Tom Kurtzman, 2016, The journal of physical chemistry. B.

Toward the Design of Mutation‐Resistant Enzyme Inhibitors: Further Evaluation of the Substrate Envelope Hypothesis

Viney Lather, Michael K Gilson, Visvaldas Kairys, 2009, Chemical biology & drug design.

Theory of Free Energy and Entropy in Noncovalent Binding

Michael K. Gilson, Huan-Xiang Zhou, M. Gilson, 2009 .

ASAP, a systematic annotation package for community analysis of genomes

Michael K. Gilson, Aaron E. Darling, Jeremy D. Glasner, 2003, Nucleic Acids Res..

Enhanced docking with the mining minima optimizer: Acceleration and side‐chain flexibility

Michael K. Gilson, Visvaldas Kairys, M. Gilson, 2002, J. Comput. Chem..

Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

Michael K Gilson, Tom Kurtzman, Kamran Haider, 2018, Journal of chemical theory and computation.

Experimental characterization of the association of β-cyclodextrin and eight novel cyclodextrin derivatives with two guest compounds

M. Gilson, B. Duggan, D. Slochower, 2020, Journal of Computer-Aided Molecular Design.

Experimental Characterization of the Association of Nine Novel Cyclodextrin Derivatives with Two Guest Compounds

M. Gilson, B. Duggan, D. Slochower, 2020 .

Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative.

Niel M. Henriksen, D. Mobley, M. Gilson, 2019, Journal of chemical theory and computation.

Bind3P: Optimization of a Water Model Based on Host-Guest Binding Data.

Michael K Gilson, Niel M. Henriksen, Jian Yin, 2018, Journal of chemical theory and computation.

Accounting for Apparent Deviations between Calorimetric and van’t Hoff Enthalpies

Niel M. Henriksen, M. Gilson, S. Kantonen, 2017, bioRxiv.

Binding enthalpy calculations for a neutral host-guest pair yield widely divergent salt effects across water models.

Andrew T. Fenley, Michael K Gilson, Niel M. Henriksen, 2015, Journal of chemical theory and computation.

The SAMPL4 host–guest blind prediction challenge: an overview

David L. Mobley, Michael K. Gilson, Andrew T. Fenley, 2014, Journal of Computer-Aided Molecular Design.

Blind prediction of host–guest binding affinities: a new SAMPL3 challenge

Michael K. Gilson, Hari S. Muddana, Christopher W. Bielawski, 2012, Journal of Computer-Aided Molecular Design.

Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Jian Yin, David L. Mobley, Michael K. Gilson, 2016, bioRxiv.

Overcoming dissipation in the calculation of standard binding free energies by ligand extraction

Michael K. Gilson, Camilo Velez-Vega, M. Gilson, 2013, J. Comput. Chem..

Fast Assignment of Accurate Partial Atomic Charges: An Electronegativity Equalization Method that Accounts for Alternate Resonance Forms

Michael K. Gilson, Hillary S. R. Gilson, Michael J. Potter, 2003, J. Chem. Inf. Comput. Sci..

Quantum Mechanical Calculation of Noncovalent Interactions: A Large-Scale Evaluation of PMx, DFT, and SAPT Approaches

Michael K. Gilson, Hari S. Muddana, Amanda Li, 2014, Journal of chemical theory and computation.

Supramolecular assembly promotes the electrocatalytic reduction of carbon dioxide by Re(I) bipyridine catalysts at a lower overpotential.

M. Gilson, C. Kubiak, F. Tezcan, 2014, Journal of the American Chemical Society.

Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method

Jian Yin, Michael K. Gilson, Andrew T. Fenley, 2014, Journal of Computer-Aided Molecular Design.

Modeling Protein-Ligand Binding by Mining Minima.

Wei Chen, Michael K Gilson, Simon P Webb, 2010, Journal of chemical theory and computation.

Identification of Symmetries in Molecules and Complexes.

M. Gilson, Wei Chen, Jing Huang, 2004 .

Tork: Conformational analysis method for molecules and complexes

Michael K. Gilson, Chia-En Chang, M. Gilson, 2003, J. Comput. Chem..

Intramolecular versus Intermolecular Hydrogen Bonding in the Adsorption of Aromatic Alcohols onto an Acrylic Ester Sorbent

M. Gilson, K. Mardis, P. Vishwanath, 2000 .

Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field

Michael R. Shirts, Matt W. Thompson, Joshua T. Horton, 2023, Journal of chemical theory and computation.

Design of Mutation‐resistant HIV Protease Inhibitors with the Substrate Envelope Hypothesis

Hong Cao, Bruce Tidor, Michael K Gilson, 2007, Chemical biology & drug design.

Absolute binding free energy calculations improve enrichment of actives in virtual compound screening

M. Gilson, G. Heinzelmann, Mudong Feng, 2022, Scientific Reports.

Fast Equilibration of Water between Buried Sites and the Bulk by Molecular Dynamics with Parallel Monte Carlo Water Moves on Graphical Processing Units.

M. Gilson, W. Sherman, I. Ben-Shalom, 2021, Journal of Chemical Theory and Computation.

Force and Stress along Simulated Dissociation Pathways of Cucurbituril-Guest Systems.

Michael K Gilson, Camilo Velez-Vega, M. Gilson, 2012, Journal of chemical theory and computation.

Screening Drug-Like Compounds by Docking to Homology Models: A Systematic Study

Michael K. Gilson, Miguel X. Fernandes, Visvaldas Kairys, 2006, J. Chem. Inf. Model..

A simple method for automated equilibration detection in molecular simulations

D. Mobley, M. Gilson, 2015 .

Symmetry numbers for rigid, flexible, and fluxional molecules: theory and applications.

Michael K Gilson, M. Gilson, K. Irikura, 2010, The journal of physical chemistry. B.

Automated docking refinement and virtual compound screening with absolute binding free energy calculations

Michael K. Gilson, Germano Heinzelmann, M. Gilson, 2020, bioRxiv.

The SAMPL5 host–guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method

Jian Yin, Michael K. Gilson, David R. Slochower, 2016, Journal of Computer-Aided Molecular Design.

The determinants of pK(a)s in proteins

Michael K. Gilson, J. A. McCammon, M. Gilson, 1996 .

Thermodynamic and Differential Entropy under a Change of Variables

Michael K. Gilson, Vladimir Hnizdo, M. Gilson, 2010, Entropy.

Differential Adsorption of Phenol Derivatives onto a Polymeric Sorbent: A Combined Molecular Modeling and Experimental Study

M. Gilson, K. Mardis, A. Glemza, 1999 .

The Binding Database: data management and interface design

Xi Chen, Ming Liu, Michael K. Gilson, 2002, Bioinform..

Bio-inspired CO2 reduction by a rhenium tricarbonyl bipyridine-based catalyst appended to amino acids and peptidic platforms: incorporating proton relays and hydrogen-bonding functional groups.

M. Gilson, C. Kubiak, F. Tezcan, 2017, Faraday discussions.

Evaluating the Accuracy of the Quasiharmonic Approximation.

Michael K Gilson, M. Gilson, Chia-En Chang, 2005, Journal of chemical theory and computation.

The ubiquity of directional and reciprocating motion in enzymes out of equilibrium

M. Gilson, D. Slochower, 2017 .

Structure and Thermodynamics of Molecular Hydration via Grid Inhomogeneous Solvation Theory

Michael K. Gilson, Crystal Nguyen, M. Gilson, 2011, 1108.4876.

Sampling conformations in high dimensions using low-dimensional distribution functions.

Michael K Gilson, Sandeep Somani, M. Gilson, 2009, The Journal of chemical physics.

Data-Driven Mapping of Gas-Phase Quantum Calculations to General Force Field Lennard-Jones Parameters.

Niel M. Henriksen, M. Gilson, Lee‐Ping Wang, 2020, Journal of chemical theory and computation.

The SAMPL4 hydration challenge: evaluation of partial charge sets with explicit-water molecular dynamics simulations

Michael K. Gilson, Andrew T. Fenley, Hari S. Muddana, 2014, Journal of Computer-Aided Molecular Design.

Efficient calculation of configurational entropy from molecular simulations by combining the mutual‐information expansion and nearest‐neighbor methods

Jun Tan, Michael K. Gilson, Vladimir Hnizdo, 2008, J. Comput. Chem..

Development of Highly Selective Epoxyketone-based Plasmodium Proteasome Inhibitors with Negligible Cytotoxicity

E. Winzeler, M. Gilson, W. Gerwick, 2022, bioRxiv.

Simulation of charge-mutant acetylcholinesterases.

M. Gilson, J. Antosiewicz, J. Mccammon, 1995, Biochemistry.

pKa measurements from nuclear magnetic resonance for the B1 and B2 immunoglobulin G-binding domains of protein G: comparison with calculated values for nuclear magnetic resonance and X-ray structures.

M. Gilson, J. Antosiewicz, P. Alexander, 1997, Biochemistry.

Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and Biomolecules

Michael K. Gilson, Andrew T. Fenley, Hari S. Muddana, 2014, PloS one.

HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants.

Hong Cao, Bruce Tidor, Michael K Gilson, 2008, Journal of the American Chemical Society.

Digital chemistry in the Journal of Medicinal Chemistry.

Michael K Gilson, M. Gilson, Shaomeng Wang, 2014, Journal of medicinal chemistry.

Evaluation of the substrate envelope hypothesis for inhibitors of HIV‐1 protease

Michael K Gilson, Visvaldas Kairys, Miguel X Fernandes, 2007, Proteins.

CACHE (Critical Assessment of Computational Hit-finding Experiments): A public–private partnership benchmarking initiative to enable the development of computational methods for hit-finding

Tudor I. Oprea, Rommie E. Amaro, Yoshua Bengio, 2021, Nature Reviews Chemistry.

Discovering de novo peptide substrates for enzymes using machine learning

P. Frazier, Jialei Wang, M. Gilson, 2018, Nature Communications.

Using Protein Homology Models for Structure-Based Studies: Approaches to Model Refinement

V. Kairys, M.K. Gilson, Miguel Xavier Fernandes, 2006, TheScientificWorldJournal.

Broadening the Horizon – Level 2.5 of the HUPO-PSI Format for Molecular Interactions

Gary D Bader, Antony F. Quinn, Peter M Woollard, 2007 .

Development of Potent and Highly Selective Epoxyketone-based Plasmodium Proteasome Inhibitors.

E. Winzeler, M. Gilson, W. Gerwick, 2023, Chemistry.

Additivity in the analysis and design of HIV protease inhibitors.

Bruce Tidor, Michael K Gilson, Akbar Ali, 2009, Journal of medicinal chemistry.

Charge Optimization Theory for Induced-Fit Ligands

B. Tidor, M. Gilson, Yang Shen, 2012, Journal of chemical theory and computation.

Charge Optimization Theory for Induced-Fit Ligands Citation

B. Tidor, M. Gilson, Yang Shen, 2012 .

Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions

Gary D Bader, Antony F. Quinn, Peter M Woollard, 2007, BMC Biology.

Discovering de novo peptide substrates for enzymes using machine learning

Michael K Gilson, Pu Yang, Matthew Thompson, 2018, Nature Communications.

Strength of Solvent-Exposed Salt-Bridges†

M. Gilson, R. Luo, L. David, 1999 .

Results of the 2017 Roadmap survey of the Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenge community

David L. Mobley, Michael K. Gilson, John Chodera, 2017 .

Modeling Molecular Recognition: Theory and Application

M K Gilson, M. Gilson, R. Luo, 2000, Journal of biomolecular structure & dynamics.

Enhanced Diffusion and Chemotaxis of Enzymes.

M. Gilson, Mudong Feng, 2019, Annual review of biophysics.

Niel M. Henriksen, M. Gilson, Andreas Hansen, 2017, The journal of physical chemistry. B.

Simulating Water Exchange to Buried Binding Sites.

M. Gilson, R. Walker, I. Ben-Shalom, 2018, Journal of chemical theory and computation.

Binding of tacrine and 6‐chlorotacrine by acetylcholinesterase

T. Straatsma, M. Gilson, J. Briggs, 1996 .

Ions and inhibitors in the binding site of HIV protease: comparison of Monte Carlo simulations and the linearized Poisson-Boltzmann theory.

M. Gilson, B. Eisenberg, D. Henderson, 2009, Biophysical journal.

Responsibility of Co-Authors

M. Gilson, M. Gilson, 1997, Science.